Install necessary packages
#install.packages("plotly")
library(plotly)
## Loading required package: ggplot2
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## Attaching package: 'plotly'
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## last_plot
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## filter
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## layout
1. Load in Data for target species
load("Prediction_Data.Rdata") #The raw IntaRNA energy table for the target species
load("Top_Proteins_DF.Rdata") #Top miRNA and targeting score for each protein in the target pathogen
load("Energy_HM_Data.Rdata") #Energy scores for interactions between top 10% of miRNAs and all proteins in target pathogen
2. Calculate summary statistics for energy scores of each human
miRNA across all genes in the target pathogen
#'Top miRNAs' panel in 'Summary View' of Rocket-miR application
IntaRNA_Data <- PG_Prediction_Data[,c(1:630)]
Top_miRNAs_DF <- data.frame(unlist(apply(IntaRNA_Data, 2, mean, na.rm = TRUE)),
unlist(apply(IntaRNA_Data, 2, median, na.rm = TRUE)),
unlist(apply(IntaRNA_Data, 2, min, na.rm = TRUE)))
colnames(Top_miRNAs_DF) <- c("Mean Energy Score", "Median Energy Score", "Minimum Energy Score")
Top_miRNAs_DF[order(Top_miRNAs_DF$`Mean Energy Score`),]
3. Visualize all individual targeting scores for each gene by all
miRNAs
#'Energy Score Heat Map' panel in 'Summary View' of Rocket-miR application
plot_ly(z = as.matrix(Energy_HM_Data), type = "heatmap"
) %>% layout(plot_bgcolor='#e5ecf6',
xaxis = list(
title='miRNA',
zerolinecolor = '#ffff',
zerolinewidth = 2,
gridcolor = 'ffff',
showticklabels = FALSE),
yaxis = list(
title='Protein Target',
zerolinecolor = '#ffff',
zerolinewidth = 2,
gridcolor = 'ffff',
showticklabels = FALSE)) %>%
add_trace(type = "heatmap", x = colnames(Energy_HM_Data[,c(1:63)]), y = Energy_HM_Data[,64]) %>%
hide_colorbar()
## Warning in RColorBrewer::brewer.pal(N, "Set2"): n too large, allowed maximum for palette Set2 is 8
## Returning the palette you asked for with that many colors
## Warning: `textfont.color` does not currently support multiple values.
## Warning: `textfont.color` does not currently support multiple values.
#Note: In this version of the plot, a darker blue color indicates a stronger energy score, while a darker red color indicates a weaker energy score
4. Identify the individual miRNA predicted to best target each
individual protein
#'Top Targeted Proteins' panel in 'Summary View' of Rocket-miR application
Top_Proteins_DF[order(Top_Proteins_DF$`Best Energy Score`),]